Dear Pang xueqin,
You could follow two different approaches for your organic structure:
1) You use parm99 FF atom types (with capital letters): you need to
load the "parm99.dat" file in LEaP to load all the required FF
parameters.
source leaprc.ff99SB
MOL = loadmol2 YOUR-MOL.mol2
saveamberparm MOL MOL.top MOL.crd
=> LEaP will not save the prmtop/prmcrd files - if missing FF
parameters are found, but LEaP will list the missing force field
parameters.
For instance, you have the CA-HA FF parameters describing the CA-HA
bond in your frcmod file: This "CA-HA" FF parameters should be in
parm99.dat; you should not need to add them in your frcmod file.
Then, you create a frcmod file with these missing FF parameters (if
LEaP detects missing FF parameters) that you load in a second step:
source leaprc.ff99SB
FRCMOD = loadamberparams your-frcmod-file
MOL = loadmol2 YOUR-MOL.mol2
saveamberparm MOL MOL.top MOL.crd
2) You use GAFF FF atom types: you need to use low case FF atom types.
Finally, a mol2 file can be used as a prep file: You should not need
to create prep file.
I hope this helps.
regards, Francois
> I am trying to get a prep field for an organic molecular
> C16H15N7O2,. with RED-III according to its tutorial. How every after
> parmchk, the frcmod give too many undefined parameter.
> So, can the prep and frcmod field be used, if not how can I solve
> this problem.
>
> Thank you for your kind help
>
> Pang xueqin
>
> Dalian ICP ACS CHINA
>
> Following are the frcmod for this molecular:
> remark goes here
> MASS
> CA 12.010 0.360 same as c2
> HA 1.008 0.135 same as hc
> OH 16.000 0.465 same as oh
> HO 1.008 0.135 same as ho
> CT 12.010 0.878 same as c3
> HC 1.008 0.135 same as hc
> H1 1.008 0.135 same as hc
> N2 14.010 0.530 same as n3
> H 1.008 0.161 same as hn
> CB 12.010 0.360 same as c2
> NA 14.010 0.530 same as na
> CR 12.010 0.360 same as c2
> C* 12.010 0.360 same as c2
> H4 1.008 0.135 same as ha
> OS 16.000 0.465 same as os
> BOND
> CA-HA 344.30 1.087 same as c2-hc
> CA-CA 478.40 1.387 same as ca-ca
> CA-OH 425.40 1.333 same as c2-oh
> OH-HO 369.60 0.974 same as ho-oh
> CA-CT 328.30 1.508 same as c2-c3
> CT-HC 337.30 1.092 same as c3-hc
> CT-CT 303.10 1.535 same as c3-c3
> CT-H1 337.30 1.092 same as c3-hc
> CT-N2 320.60 1.470 same as c3-n3
> N2-H 394.10 1.018 same as hn-n3
> N2-CA 449.00 1.364 same as ca-nh
> N2-CB 449.00 1.364 same as cc-nh
> N2-CR 449.00 1.364 same as cc-nh
> N2-NA 426.70 1.420 same as n3-na
> NA-H 406.60 1.011 same as hn-na
> NA-CR 411.10 1.391 same as c2-na
> CR-C* 418.30 1.429 same as cc-cc
> C*-C* 418.30 1.429 same as cc-cc
> C*-OS 392.60 1.357 same as c2-os
> C*-HA 344.30 1.087 same as c2-hc
> C*-CA 411.70 1.434 same as ca-cc
> CA-H4 344.30 1.087 same as c2-ha
> CA-OS 392.60 1.357 same as c2-os
> ANGLE
> CA-CA-HA 50.300 119.700 same as c2-c2-hc
> CA-CA-CA 67.200 119.970 same as ca-ca-ca
> CA-CA-CT 64.300 123.420 same as c2-c2-c3
> CA-CA-OH 71.600 122.280 same as c2-c2-oh
> CA-OH-HO 49.900 108.980 same as c2-oh-ho
> CA-CT-HC 47.000 110.490 same as c2-c3-hc
> CA-CT-CT 63.700 110.960 same as c2-c3-c3
> CT-CT-H1 46.400 110.050 same as c3-c3-hc
> CT-CT-N2 66.200 110.380 same as c3-c3-n3
> HC-CT-HC 39.400 108.350 same as hc-c3-hc
> HC-CT-CT 46.400 110.050 same as c3-c3-hc
> CT-N2-H 47.100 109.920 same as c3-n3-hn
> CT-N2-CA 62.820 117.790 Calculated with empirical approach
> H1-CT-H1 39.400 108.350 same as hc-c3-hc
> H1-CT-N2 49.400 109.800 same as hc-c3-n3
> N2-CA-N2 71.400 120.980 same as nh-ca-nh
> H -N2-CA 49.100 119.380 same as c2-n3-hn
> CA-N2-CA 64.300 127.460 same as ca-nh-ca
> CA-N2-CB 66.200 124.680 same as c2-n3-c2
> CA-N2-NA 66.760 118.340 Calculated with empirical approach
> H -N2-H 41.300 107.130 same as hn-n3-hn
> N2-CB-N2 72.900 115.960 same as nh-cc-nh
> H -N2-CB 49.100 119.380 same as c2-n3-hn
> CB-N2-CR 66.200 124.680 same as c2-n3-c2
> CB-N2-NA 66.760 118.340 Calculated with empirical approach
> N2-CR-NA 73.125 113.900 Calculated with empirical approach
> N2-CR-C* 68.600 118.980 same as cc-cc-nh
> H -N2-CR 49.100 119.380 same as c2-n3-hn
> N2-NA-H 36.098 120.400 Calculated with empirical approach
> N2-NA-CR 64.600 124.800 same as c2-na-n3
> NA-CR-C* 69.800 121.380 same as c2-c2-na
> H -NA-CR 47.600 119.280 same as c2-na-hn
> CR-C*-C* 67.900 110.700 same as cc-cc-cc
> CR-C*-OS 71.200 121.430 same as c2-c2-os
> C*-C*-HA 50.300 119.700 same as c2-c2-hc
> C*-C*-C* 67.900 110.700 same as cc-cc-cc
> C*-OS-CA 66.000 113.140 same as c2-os-c2
> C*-C*-OS 71.200 121.430 same as c2-c2-os
> C*-C*-CA 67.700 111.040 same as ca-cc-cc
> C*-CA-H4 50.000 120.940 same as c2-c2-ha
> C*-CA-OS 71.200 121.430 same as c2-c2-os
> HA-C*-CA 50.300 119.700 same as c2-c2-hc
> H4-CA-OS 52.400 112.690 same as ha-c2-os
> DIHE
> CA-CA-CA-OH 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> CA-CA-CA-CA 1 3.625 180.000 2.000 same as
> X -ca-ca-X
> CA-CA-CA-HA 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> CA-CA-CT-HC 1 0.380 180.000 -3.000 same as
> hc-c3-c2-c2
> CA-CA-CT-HC 1 1.150 0.000 1.000 same as
> hc-c3-c2-c2
> CA-CA-CT-CT 1 0.000 0.000 2.000 same as
> X -c2-c3-X
> HA-CA-CA-HA 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> HA-CA-CA-CT 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> CA-CA-CA-CT 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> CA-CA-OH-HO 1 1.050 180.000 2.000 same as
> X -c2-oh-X
> HA-CA-CA-OH 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> CA-CT-CT-H1 1 0.156 0.000 3.000 same as
> X -c3-c3-X
> CA-CT-CT-N2 1 0.156 0.000 3.000 same as
> X -c3-c3-X
> CT-CT-N2-H 1 0.300 0.000 3.000 same as
> X -c3-n3-X
> CT-CT-N2-CA 1 0.300 0.000 3.000 same as
> X -c3-n3-X
> HC-CT-CT-H1 1 0.150 0.000 3.000 same as
> hc-c3-c3-hc
> HC-CT-CT-N2 1 0.156 0.000 3.000 same as
> X -c3-c3-X
> CT-N2-CA-N2 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> H1-CT-N2-H 1 0.300 0.000 3.000 same as
> X -c3-n3-X
> H1-CT-N2-CA 1 0.300 0.000 3.000 same as
> X -c3-n3-X
> N2-CA-N2-H 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> N2-CA-N2-CA 1 1.050 180.000 2.000 same as
> X -ca-nh-X
> N2-CA-N2-CB 1 1.050 180.000 2.000 same as
> X -ca-nh-X
> CA-N2-CB-N2 1 1.050 180.000 2.000 same as
> X -cc-nh-X
> N2-CA-N2-NA 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> CA-N2-NA-H 1 1.600 0.000 2.000 same as
> X -n3-na-X
> CA-N2-NA-CR 1 1.600 0.000 2.000 same as
> X -n3-na-X
> N2-CB-N2-H 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> N2-CB-N2-CR 1 1.050 180.000 2.000 same as
> X -cc-nh-X
> N2-CB-N2-NA 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> CB-N2-CR-NA 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> CB-N2-CR-C* 1 1.050 180.000 2.000 same as
> X -cc-nh-X
> CB-N2-NA-H 1 1.600 0.000 2.000 same as
> X -n3-na-X
> CB-N2-NA-CR 1 1.600 0.000 2.000 same as
> X -n3-na-X
> N2-CR-NA-N2 1 0.625 180.000 2.000 same as
> X -c2-na-X
> N2-CR-NA-H 1 0.625 180.000 2.000 same as
> X -c2-na-X
> N2-CR-C*-C* 1 4.000 180.000 2.000 same as
> X -cc-cc-X
> N2-CR-C*-OS 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> H -N2-CR-NA 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> H -N2-CR-C* 1 0.300 180.000 2.000 same as
> X -c2-n3-X
> N2-NA-CR-C* 1 0.625 180.000 2.000 same as
> X -c2-na-X
> NA-CR-C*-C* 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> NA-CR-C*-OS 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> H -NA-CR-C* 1 0.625 180.000 2.000 same as
> X -c2-na-X
> CR-C*-C*-HA 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> CR-C*-C*-C* 1 4.000 180.000 2.000 same as
> X -cc-cc-X
> CR-C*-OS-CA 1 1.050 180.000 2.000 same as
> X -c2-os-X
> C*-C*-C*-HA 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> C*-C*-C*-CA 1 4.000 180.000 2.000 same as
> X -cc-cc-X
> C*-OS-CA-C* 1 1.050 180.000 2.000 same as
> X -c2-os-X
> C*-OS-CA-H4 1 1.050 180.000 2.000 same as
> X -c2-os-X
> C*-C*-OS-CA 1 1.050 180.000 2.000 same as
> X -c2-os-X
> C*-C*-CA-H4 1 4.000 180.000 2.000 same as
> X -cc-cc-X
> C*-C*-CA-OS 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> HA-C*-C*-OS 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> HA-C*-C*-HA 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> HA-C*-C*-CA 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> C*-C*-C*-OS 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> HA-C*-CA-H4 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> HA-C*-CA-OS 1 6.650 180.000 2.000 same as
> X -c2-c2-X
> IMPROPER
> CA-CA-CA-HA 1.1 180.0 2.0 Using
> default value
> CA-CA-CA-OH 1.1 180.0 2.0 Using
> default value
> CA-CA-CA-CT 1.1 180.0 2.0 Using
> default value
> CA-CT-N2-H 1.1 180.0 2.0 Using
> default value
> N2-N2-CA-N2 1.1 180.0 2.0 Using
> default value
> CA-CA-N2-H 1.1 180.0 2.0 Using
> default value
> CA-H -N2-H 1.1 180.0 2.0 Using
> default value
> CA-CB-N2-H 1.1 180.0 2.0 Using
> default value
> N2-N2-CB-N2 1.1 180.0 2.0 Using
> default value
> CB-CR-N2-H 1.1 180.0 2.0 Using
> default value
> CA-CB-N2-NA 1.1 180.0 2.0 Using
> default value
> CR-H -NA-N2 1.1 180.0 2.0 Using
> default value
> C*-N2-CR-NA 1.1 180.0 2.0 Using
> default value
> C*-CR-C*-OS 1.1 180.0 2.0 Using
> default value
> C*-C*-C*-HA 1.1 180.0 2.0 Using
> default value
> C*-CA-C*-HA 1.1 180.0 2.0 Using
> default value
> C*-H4-CA-OS 1.1 180.0 2.0 Using
> default value
> NONBON
> CA 1.9080 0.0860 same as ca
> HA 1.4870 0.0157 same as hc
> OH 1.7210 0.2104 same as oh
> HO 0.0000 0.0000 same as ho
> CT 1.9080 0.1094 same as c3
> HC 1.4870 0.0157 same as hc
> H1 1.4870 0.0157 same as hc
> N2 1.8240 0.1700 same as nh
> H 0.6000 0.0157 same as hn
> CB 1.9080 0.0860 same as cc
> NA 1.8240 0.1700 same as na
> CR 1.9080 0.0860 same as cc
> C* 1.9080 0.0860 same as cc
> H4 1.4870 0.0157 same as hc
> OS 1.6837 0.1700 same as os
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Received on Thu Oct 22 2009 - 03:00:03 PDT
